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- PDB-5nki: Crystal Structure of Ephrin A2 (EphA2) Receptor Protein Kinase wi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5nki | ||||||
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Title | Crystal Structure of Ephrin A2 (EphA2) Receptor Protein Kinase with Compound 4b | ||||||
![]() | Ephrin type-A receptor 2 | ||||||
![]() | TRANSFERASE / Inhibitor / Complex / Protein Tyrosine Kinase | ||||||
Function / homology | ![]() notochord cell development / notochord formation / lens fiber cell morphogenesis / blood vessel endothelial cell proliferation involved in sprouting angiogenesis / negative regulation of lymphangiogenesis / axial mesoderm formation / pericyte cell differentiation / cAMP metabolic process / positive regulation of bicellular tight junction assembly / regulation of blood vessel endothelial cell migration ...notochord cell development / notochord formation / lens fiber cell morphogenesis / blood vessel endothelial cell proliferation involved in sprouting angiogenesis / negative regulation of lymphangiogenesis / axial mesoderm formation / pericyte cell differentiation / cAMP metabolic process / positive regulation of bicellular tight junction assembly / regulation of blood vessel endothelial cell migration / leading edge membrane / negative regulation of chemokine production / post-anal tail morphogenesis / bone remodeling / transmembrane-ephrin receptor activity / response to growth factor / tight junction / activation of GTPase activity / regulation of lamellipodium assembly / branching involved in mammary gland duct morphogenesis / EPH-Ephrin signaling / neural tube development / RND1 GTPase cycle / RND2 GTPase cycle / RND3 GTPase cycle / mammary gland epithelial cell proliferation / RHOV GTPase cycle / EPHA-mediated growth cone collapse / growth factor binding / regulation of cell adhesion mediated by integrin / lamellipodium membrane / RHOU GTPase cycle / RHOG GTPase cycle / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / RAC2 GTPase cycle / RAC3 GTPase cycle / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / vasculogenesis / regulation of angiogenesis / keratinocyte differentiation / RAC1 GTPase cycle / transmembrane receptor protein tyrosine kinase activity / negative regulation of angiogenesis / phosphatidylinositol 3-kinase/protein kinase B signal transduction / regulation of ERK1 and ERK2 cascade / osteoclast differentiation / cell chemotaxis / skeletal system development / molecular function activator activity / protein localization to plasma membrane / cell motility / positive regulation of protein localization to plasma membrane / axon guidance / receptor protein-tyrosine kinase / ruffle membrane / osteoblast differentiation / intrinsic apoptotic signaling pathway in response to DNA damage / cell migration / lamellipodium / virus receptor activity / receptor complex / cell adhesion / defense response to Gram-positive bacterium / positive regulation of cell migration / inflammatory response / cadherin binding / phosphorylation / focal adhesion / dendrite / cell surface / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kudlinzki, D. / Linhard, V.L. / Witt, K. / Gande, S.L. / Saxena, K. / Heinzlmeir, S. / Medard, G. / Kuester, B. / Schwalbe, H. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Chemoproteomics-Aided Medicinal Chemistry for the Discovery of EPHA2 Inhibitors. Authors: Heinzlmeir, S. / Lohse, J. / Treiber, T. / Kudlinzki, D. / Linhard, V. / Gande, S.L. / Sreeramulu, S. / Saxena, K. / Liu, X. / Wilhelm, M. / Schwalbe, H. / Kuster, B. / Medard, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 78.1 KB | Display | ![]() |
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PDB format | ![]() | 56.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 981.8 KB | Display | ![]() |
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Full document | ![]() | 986.6 KB | Display | |
Data in XML | ![]() | 14.7 KB | Display | |
Data in CIF | ![]() | 21.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5njzC ![]() 5nk0C ![]() 5nk1C ![]() 5nk2C ![]() 5nk3C ![]() 5nk4C ![]() 5nk5C ![]() 5nk6C ![]() 5nk7C ![]() 5nk8C ![]() 5nk9C ![]() 5nkaC ![]() 5nkbC ![]() 5nkcC ![]() 5nkdC ![]() 5nkeC ![]() 5nkfC ![]() 5nkgC ![]() 5nkhC ![]() 5i9uS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 34462.840 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P29317, receptor protein-tyrosine kinase |
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#2: Chemical | ChemComp-8ZW / ~{ |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.94 Å3/Da / Density % sol: 36.45 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 37.5% MPD/PEG1000/PEG3350 (MD), 0.1 M Amino Acids Mix (MD), 0.1 M Hepes pH6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 5, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9199 Å / Relative weight: 1 |
Reflection | Resolution: 1.675→38.166 Å / Num. obs: 29586 / % possible obs: 98.2 % / Redundancy: 4.2 % / Biso Wilson estimate: 24.16 Å2 / Rrim(I) all: 0.116 / Net I/σ(I): 9.66 |
Reflection shell | Resolution: 1.68→1.78 Å / Mean I/σ(I) obs: 1.86 / % possible all: 95.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5I9U Resolution: 1.675→38.166 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 18.8
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.675→38.166 Å
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Refine LS restraints |
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LS refinement shell |
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